Variant report

Variant	rs12563539
Chromosome Location	chr1:153961784-153961785
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:153745179..153749280-chr1:153961747..153968478,7	MCF-7	breast:
2	chr1:153699974..153702840-chr1:153961694..153964834,3	K562	blood:
3	chr1:153642259..153645171-chr1:153961754..153965588,6	K562	blood:
4	chr1:153961765..153965852-chr1:154152407..154156955,8	K562	blood:
5	chr1:153961745..153965852-chr1:154153352..154156776,9	K562	blood:
6	chr1:153905142..153906836-chr1:153961384..153963973,2	K562	blood:
7	chr1:153642202..153645171-chr1:153961721..153964784,6	K562	blood:
8	chr1:153629459..153632821-chr1:153961630..153966753,5	K562	blood:
9	chr1:153890756..153897034-chr1:153961597..153964863,14	K562	blood:

No data

Variant related genes	Relation type
ENSG00000143614	Chromatin interaction
ENSG00000143621	Chromatin interaction
ENSG00000143549	Chromatin interaction
ENSG00000143554	Chromatin interaction
ENSG00000143553	Chromatin interaction
ENSG00000143624	Chromatin interaction
ENSG00000198837	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs12564199	0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs73010774	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999364	chr1:153622634-154419436	Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
2	nsv535175	chr1:153622634-154419436	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
3	nsv532551	chr1:153732039-154192279	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	233 gene(s)	inside rSNPs	diseases
4	esv1830240	chr1:153885261-154370938	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	239 gene(s)	inside rSNPs	diseases
5	esv3453878	chr1:153960428-153962010	Weak transcription	Chromatin interactive region	18 gene(s)	inside rSNPs	diseases
6	esv3453879	chr1:153960712-153962003	Weak transcription	Chromatin interactive region	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153958600-153962800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr1:153958800-153962600	Weak transcription	Lung	lung
3	chr1:153958800-153962600	Weak transcription	Spleen	Spleen
4	chr1:153958800-153962800	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr1:153959000-153962600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr1:153959200-153962600	Weak transcription	Pancreas	Pancrea
7	chr1:153959200-153963200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr1:153959200-153963200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr1:153959400-153962600	Weak transcription	Fetal Muscle Trunk	muscle
10	chr1:153959400-153962600	Weak transcription	Placenta	Placenta
11	chr1:153959400-153962800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr1:153959400-153963200	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr1:153959600-153962400	Weak transcription	Primary T helper cells fromperipheralblood	blood
14	chr1:153959600-153962400	Weak transcription	Brain Germinal Matrix	brain
15	chr1:153959600-153962400	Weak transcription	Colon Smooth Muscle	Colon
16	chr1:153959600-153962600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr1:153959600-153962600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr1:153959600-153962600	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr1:153959600-153962600	Weak transcription	Brain Cingulate Gyrus	brain
20	chr1:153959600-153962600	Weak transcription	Fetal Brain Male	brain
21	chr1:153959600-153962800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr1:153959600-153962800	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr1:153959600-153962800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr1:153959600-153962800	Weak transcription	Adipose Nuclei	Adipose
25	chr1:153959600-153962800	Weak transcription	Liver	Liver
26	chr1:153959600-153962800	Weak transcription	Brain Angular Gyrus	brain
27	chr1:153959600-153962800	Weak transcription	Colonic Mucosa	Colon
28	chr1:153959600-153962800	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr1:153959600-153962800	Weak transcription	Fetal Kidney	kidney
30	chr1:153959600-153962800	Weak transcription	Fetal Lung	lung
31	chr1:153959600-153962800	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr1:153959600-153962800	Weak transcription	HSMM	muscle
33	chr1:153959600-153962800	Weak transcription	HUVEC	blood vessel
34	chr1:153959600-153962800	Weak transcription	Osteobl	bone
35	chr1:153959600-153963000	Weak transcription	Fetal Heart	heart
36	chr1:153959800-153962400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
37	chr1:153959800-153962400	Weak transcription	Primary neutrophils fromperipheralblood	blood
38	chr1:153959800-153962400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
39	chr1:153959800-153962400	Weak transcription	Primary T helper cells PMA-I stimulated	--
40	chr1:153959800-153962400	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr1:153959800-153962400	Weak transcription	Dnd41	blood
42	chr1:153959800-153962400	Weak transcription	K562	blood
43	chr1:153959800-153962600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr1:153959800-153962600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr1:153959800-153962600	Weak transcription	Brain Anterior Caudate	brain
46	chr1:153959800-153962600	Weak transcription	Fetal Muscle Leg	muscle
47	chr1:153959800-153962600	Weak transcription	Fetal Stomach	stomach
48	chr1:153959800-153962600	Weak transcription	A549	lung
49	chr1:153959800-153962600	Weak transcription	NHLF	lung
50	chr1:153959800-153962800	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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